SIVIC: Open source DICOM MR Spectroscopy Framework for Researchers, and Radiologists

DICOM May 15, 2019

SIVIC is an open source framework for medical imaging (DICOM MR Spectroscopy)  processing and visualization.  SIVIC provides many features to facilitate processing and analysis of the MRS (MR Spectroscopy) imaging as it also provides a Horos plugin to ease image sharing, transfer, and processing with Horos DICOM viewer for Mac OSX users.

SIVIC development is managed by Nelson Lab which is part of  department of Radiology of UCSF (University of California, San Francisco). Nelson Lab is dedicated for development of techniques for acquisition, reconstruction, and quantitative analysis of Magnetic Resonance (MR) imaging and spectral data.

What's Magnetic resonance (MR) Spectroscopy?

Magnetic resonance (MR) spectroscopy is a noninvasive diagnostic test for measuring biochemical changes in the brain, especially the presence of tumors. Indication: It's often ordered when the cause of a lesion is unclear based on the known information.

MR spectroscopy is conducted on the same machine as a conventional MRI. Spectroscopy is a series of tests that are added to the MRI scan of a brain or spine to measure the chemical metabolism of a suspected tumor.

MR spectroscopy analyzes molecules such as hydrogen ions or protons. Proton spectroscopy is more commonly used. There are several different metabolites, or products of metabolism, that can be measured to differentiate between tumor types.

SIVIC Open source MRS Framework

SIVIC 

Despite the file size for the application, it's built with C++, but researchers/ and radiologists should be able to use its full potential as its feature-rich application that works with almost every desktop operating system.

SIVIC team offers many educational materials in their WIKI including tutorials in PDF format which include:  How to setup SIVIC for OsiriX and Horos, How to use the GUI and command-line port, Docker setup and deployment with SIVIC.

How SIVIC works. [src. HINDAW]

SIVIC Core features

  • DICOM MRS Viewer
  • DICOM MR patch file reader
  • DICOM MRS file converter
  • Multiple-readers for different files, models, machines, & extensions

SIVIC Features

  • Dynamic MRS
  • Multi-volumetric images (multi-time point or multi-channel images)
  • Perfusion visualization and DSC analysis
  • GE P-File reading (9.x-26.x, probe-p, mbrease)
  • DICOM MR Spectroscopy reading/writing
  • DICOM MR Image Storage reading
  • DICOM Secondary Capture writing
  • multi-coi, multi-time point MRS data support
  • orthogonal reformatting of MRS views
  • rendering of orthogonal color overlay planes
  • 2D/3D sat bands and volume localization visualization
  • Varian FDF reading
  • Varian fid/procpar reading
  • Siemens .rda reading (beta)
  • Single voxel multi-coil recon (prototype/demo)
  • Standalone MRS file converter (GE, Varian, Siemens -> DICOM MRS)
  • DICOM Enhanced MR Image Storage Reading
  • DICOM CT Image Storage Reading
  • Siemens.IMA (MRImageStorage) Reading
  • Metabolite Map Generation
  • Export Metabolite Maps to DICOM
  • Philips SPAR/SDAT Reader
  • Integration with LCModel
  • Multiple file formats -src.
  • Command line tools for batch processing
  • Horos plugin
SIVIC with OsiriX 

Platforms

SIVIC is available for:

  • Windows
  • Mac OSX
  • Linux

Programming language

  • C++

License

  • BSD license

Resources

Publications

  • SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows. [src]
  • SIVIC [Hindaw]: SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows [src]

DICOMResearchOpen sourceRadiologyPACSMedical ImagingMedical Simulation


Hamza Mu

A physician with programming skills, Linux user since late 1990s, Open source supporter . Doing coding with Python, NodeJS (Meteor, VueJS, Express, D3, PhantomJS), SmallTalk & R language.